Biomedical subjects

Didier Raoult

Publications and source records attributed to Didier Raoult.

At least 127 records · Page 7Linked to original sources

PubMed2005

A new example of viral intein in Mimivirus.

BACKGROUND: Inteins are "protein introns" that remove themselves from their host proteins through an autocatalytic protein-splicing. After their discovery, inteins have been quickly identified in all domains of life, but only once to date in the genome of a eukaryote-infecting virus. RESULTS: Here we report the identification and bioinformatics characterization of an intein in the DNA polymerase PolB gene of amoeba infecting Mimivirus, the largest known double-stranded DNA virus, the origin of which has been proposed to predate the emergence of eukaryotes. Mimivirus intein exhibits canonical sequence motifs and clearly belongs to a subclass of archaeal inteins always found in the same location of PolB genes. On the other hand, the Mimivirus PolB is most similar to eukaryotic Poldelta sequences. CONCLUSIONS: The intriguing association of an extremophilic archaeal-type intein with a mesophilic eukaryotic-like PolB in Mimivirus is consistent with the hypothesis that DNA viruses might have been the central reservoir of inteins throughout the course of evolution.

Amino Acid Sequence↗

PubMed2005

Quantitative histological examination of mechanical heart valves.

BACKGROUND: Histological demonstration of microorganisms, vegetations, or active endocarditis in cardiac valve tissue is included in the Duke criteria and is considered to be a criterion of confirmed infective endocarditis. However, the histological features that characterize infective endocarditis are not accurately defined at the qualitative and quantitative levels. METHODS: Pathologic analysis of tissue adjoining mechanical cardiac valves was undertaken retrospectively for 21 patients who underwent surgical removal of a mechanical valve because of suspected infective endocarditis and 69 patients who underwent surgical removal of a mechanical valve because of noninfectious dysfunction. To better define the histological criteria for infective endocarditis, we used quantitative image analysis to compare these 2 groups of patients with respect to valvular fibrosis, calcifications, vegetations, patterns of inflammation, and vascularization. RESULTS: Histologically, infective endocarditis in patients with mechanical valves was characterized by the demonstration of microorganisms, vegetations, and significant neutrophil-rich inflammatory infiltrates with extensive neovascularization. In contrast, valve tissue specimens from patients with mechanical valves that were removed because of noninfectious complications showed significant rates of extensive fibrosis and, when present, inflammatory infiltrates that were mainly composed of macrophages and lymphocytes. A neutrophil surface area with a cutoff value of > or =2% of the total valve tissue surface is highly predictive of (90%) and specific for (98%) infective endocarditis. CONCLUSIONS: When no microorganisms are detected and vegetations are lacking in tissue adjacent to a mechanical valve, neutrophil-rich inflammation and extensive neovascularization might better histologically define the term "active endocarditis" in the Duke criteria. This definition would allow differentiation between infective endocarditis and inflammatory noninfectious valve processes in patients with mechanical cardiac valves.

Acremonium↗

PubMed2005

Bartonella quintana in a 4000-year-old human tooth.

Bacteria of the genus Bartonella are transmitted by ectoparasites (lice, fleas, ticks) and have mammalian reservoirs in which they cause chronic, asymptomatic bacteremia. Humans are the reservoir of B. quintana, the louse-borne agent of trench fever. We detected DNA of B. quintana in the dental pulp of a person who died 4000 years ago.

Bartonella quintana↗

PubMed2005

A pedagogical farm as a source of Q fever in a French city.

Q fever is a worldwide zoonosis caused by Coxiella burnetii and presents as both acute or chronic cases. The disease can be transmitted from animal reservoirs to humans by inhalation of infected aerosols. A previous study had revealed a hyperendemic focus in South France. A case-control study was carried-out in this area from 1996 to 1999. Besides the role of wind, this study stressed out the exposure to a pedagogical farm as an independent risk factor (4.7% of cases - 0 controls): Exposure to sheep and new-born animals (OR: 3.07 and 4.01 respectively) were not significant after omission of people exposed to the pedagogical farm. Such farms are visited by people who would not have any other contact with farm animals. These farms require a drastic hygiene and control. Q fever, as a public health problem, still requires further studies to identify and confirm individual behavioral risk factors.

Adolescent↗

PubMed2005

Diagnosis of infectious endocarditis in patients undergoing valve surgery.

PURPOSE: Histologic examination of valve samples is considered as the gold standard for the diagnosis of infectious endocarditis. Molecular tools are also very promising for patients with negative-culture endocarditis. Thus, we studied the contribution of valvular histology, culture, and 16S rRNA PCR amplification plus sequencing to the diagnosis of infectious endocarditis in patients undergoing valve surgery. SUBJECTS AND METHODS: We performed culture, histological examination, and broad-range PCR amplification plus sequencing on valve samples taken from 127 patients with infectious endocarditis and from 118 patients without endocarditis. The sensitivity and specificity of these tests for the diagnosis of endocarditis in patients undergoing valve surgery were studied. RESULTS: The sensitivity of PCR was of 61% (64/105) whereas that of histological examination was of 63% (62/98) and that of valve culture was of only 13% (14/105). All 68 positive PCR results considered reliable according to an interpretation scheme were from patients with infectious endocarditis, resulting in a 100% (118/118) specificity of the interpreted molecular approach. The specificity of histology was also of 100% (118/118) when using stringent criteria (ie, presence of vegetation, microorganisms, and/or valvular inflammation with mainly polymorphonuclear cells). PCR identified an etiological agent in 38% (5/13) of definite blood culture-negative infectious endocarditis. CONCLUSION: We show that valvular histology with stringent criteria is the gold standard for the diagnosis of infectious endocarditis. Broad-range amplification of 16S rRNA gene is indicated for infectious endocarditis of unknown etiology, whereas valve culture is of limited sensitivity.

Adult↗

PubMed2005

Some lessons from Rickettsia genomics.

Sequencing of the Rickettsia conorii genome and its comparison with its closest sequenced pathogenic relative, i.e., Rickettsia prowazekii, provided powerful insights into the evolution of these microbial pathogens. However, advances in our knowledge of rickettsial diseases are still hindered by the difficulty of working with strict intracellular bacteria and their hosts. Information gained from comparing the genomes of closely related organisms will shed new light on proteins susceptible to be targeted in specific diagnostic assays, by new antimicrobial drugs, and that could be employed in the generation of future rickettsial vaccines. In this review we present a detailed comparison of the metabolic pathways of these bacteria as well as the polymorphisms of their membrane proteins, transporters and putative virulence factors. Environmental adaptation of Rickettsia is also discussed.

Amino Acid Sequence↗

PubMed2005

Palaeomicrobiology: current issues and perspectives.

Palaeomicrobiology is an emerging field that is devoted to the detection, identification and characterization of microorganisms in ancient remains. Data indicate that host-associated microbial DNA can survive for almost 20,000 years, and environmental bacterial DNA preserved in permafrost samples has been dated to 400,000-600,000 years. In addition to frozen and mummified soft tissues, bone and dental pulp can also be used to search for microbial pathogens. Various techniques, including microscopy and immunodetection, can be used in palaeomicrobiology, but most data have been obtained using PCR-based molecular techniques. Infections caused by bacteria, viruses and parasites have all been diagnosed using palaeomicrobiological techniques. Additionally, molecular typing of ancient pathogens could help to reconstruct the epidemiology of past epidemics and could feed into current models of emerging infections, therefore contributing to the development of appropriate preventative measures.

Animals↗

PubMed2005

Comparison of intuitive versus systematic strategies for aetiological diagnosis of pericardial effusion.

In an attempt to elucidate better the various aetiologies of pericardial effusion, we developed a diagnostic protocol that incorporated a battery of systematic tests including blood cultures, throat swab cultures and serological tests for various infectious agents and estimation of serum antinuclear antibodies and serum thyroid-stimulating hormone. Over a 2-y period ending May 2000, we evaluated prospectively and diagnostic usefulness of our strategy in a cohort (n = 136) of patients with pericardial effusion treated at Hospital Timone (HT), Marseille. We compared our findings with those observed in a retrospectively (May 1998-May 2000) drawn cohort (n = 127) of patients treated at Hospital Louis Pradel (HLP), Lyon and in which the laboratory investigation towards establishing an aetiological diagnosis was undertaken intuitively. Overall, the aetiologies were obvious clinically in 18% of cases. In other cases, specific aetiologies (27.3% vs 3.9%; p < 0.001), including treatable conditions (11.1% vs 2.4%; p < 0.001) were identified significantly more frequently in the HT cohort compared to the HLP cohort. The diagnosis strategy we propose may be helpful in elucidating the aetiological diagnosis of pericardial effusion when a cause is not obvious clinically.

Adolescent↗

PubMed2005

Experimental infection models of ticks of the Rhipicephalus sanguineus group with Rickettsia conorii.

Rhipicephalus sanguineus group ticks collected on dogs in Thailand were maintained in the laboratory over several generations to test methods to infect these ticks with Rickettsia conorii, the agent of Mediterranean spotted fever. Three methods were tested: (1) infection of adults and nymphs through artificially induced bacteremic rabbit, (2) capillary feeding of solution containing 5 x 10(3) and 5 x 10(5)pfu/mL of R. conorii to adult female ticks, and (3) immersion of engorged nymphs which were "one leg-cut," "two leg-cut," or "cuticle cut" in solution containing R. conorii. The most efficient method to infect adult ticks with R. conorii was infection of ticks through the bacteremic rabbit (71.4%). The best method to infect nymphs with R. conorii was immersion of "one leg-cut" engorged nymphs in solution containing R. conorii (30%). Interestingly, a high mortality of the ticks infected with R. conorii was observed regardless of the method used. The harmful effect of R. conorii on Rh. sanguineus group ticks from Thailand is discussed including the role of the geographic origin of the ticks and the difficulties to identify ticks within this group to the species level.

Animals↗

PubMed2005

Ectoparasitism and vector-borne diseases in 930 homeless people from Marseilles.

Homeless people are particularly exposed to ectoparasites, but their exposure to arthropod-borne diseases has not been evaluated systematically. A medical team of 27 persons (7 nurses, 6 infectious disease residents or fellows, 2 dermatologists, and 12 infectious disease specialists) visited the 2 shelters in Marseilles, France, for 4 consecutive years. Homeless volunteers were interviewed, examined, and received care; and blood was sampled for cell counts and detection of bacteremia, antibodies to louse-borne (Rickettsia prowazekii, Bartonella quintana, and Borrelia recurrentis), flea-borne (R. typhi, R. felis), mite-borne (R. akari), and tick-borne (R. conorii) bacterial agents. We selected sex- and age-adjusted controls among healthy blood donors. Over 4 years, 930 homeless people were enrolled. Lice were found in 22% and were associated with hypereosinophilia (odds ratio, 5.7; 95% confidence intervals, 1.46-22.15). Twenty-seven patients (3%) with scabies were treated with ivermectin. Bartonella quintana was isolated from blood culture in 50 patients (5.3%), 36 of whom were treated effectively. The number of bacteremic patient increased from 3.4% to 8.4% (p = 0.02) over the 4 years of the study. We detected a higher seroprevalence to Borrelia recurrentis, R. conorii, and R. prowazekii antibodies in the homeless. Our study shows a high prevalence of louse-borne infections in the homeless and a high degree of exposure to tick-borne diseases and scabies. Despite effective treatment for Bartonella quintana bacteremia and the efforts made to delouse this population, Bartonella quintana remains endemic, and we found hallmarks of epidemic typhus and relapsing fever. The uncontrolled louse infestation of this population should alert the community to the possibility of severe re-emerging louse-borne infections.

Adolescent↗

PubMed2005

Blood culture-negative endocarditis in a reference center: etiologic diagnosis of 348 cases.

To identify the current etiologies of blood culture-negative infective endocarditis and to describe the epidemiologic, clinical, laboratory, and echocardiographic characteristics associated with each etiology, as well as with unexplained cases, we tested samples from 348 patients suspected of having blood culture-negative infective endocarditis in our diagnostic center, the French National Reference Center for Rickettsial Diseases, between 1983 and 2001. Serology tests for Coxiella burnettii, Bartonella species, Chlamydia species, Legionella species, and Aspergillus species; blood culture on shell vial; and, when available, analysis of valve specimens through culture, microscopic examination, and direct PCR amplification were performed. Physicians were asked to complete a questionnaire, which was computerized. Only cases of definite infective endocarditis, as defined by the modified Duke criteria, were included. A total of 348 cases were recorded-to our knowledge, the largest series reported to date. Of those, 167 cases (48%) were associated with C. burnetii, 99 (28%) with Bartonella species, and 5 (1%) with rare, fastidious bacterial agents of endocarditis (Tropheryma whipplei, Abiotrophia elegans, Mycoplasma hominis, Legionella pneumophila). Among 73 cases without etiology, 58 received antibiotic drugs before the blood cultures. Six cases were right-sided endocarditis and 4 occurred in patients who had a permanent pacemaker. Finally, no explanatory factor was found for 5 remaining cases (1%), despite all investigations.Q fever endocarditis affected males in 75% of cases, between 40 and 70 years of age. Ninety-one percent of patients had a previous valvulopathy, 32% were immunocompromised, and 70% had been exposed to animals. Our study confirms the improved clinical presentation and prognosis of the disease observed during the last decades. Such an evolution could be related to earlier diagnosis due to better physician awareness and more sensitive diagnostic techniques. As for Bartonella species, B. quintana was recorded more frequently than B. henselae (53 vs 17 cases). For 18 patients with Bartonella endocarditis, the responsible species was not identified. Species determination was achieved through culture and/or PCR in 49 cases and through Western immunoblotting in 22. Comparison of B. quintana and B. henselae endocarditis revealed distinct epidemiologic patterns. The 2 cases due to T. whipplei reflect the emerging role of this agent as a cause of infective endocarditis. Because identification of the bacterium was possible only through analysis of excised valves by histologic examination, PCR, and culture on shell vial, the prevalence of the disease might be underestimated. Among patients who received antibiotic drugs before blood cultures, 4 cases (7%) were found to be associated with Streptococcus species (2 S. bovis and 2 S. mutans) through 16S rDNA gene amplification directly from the valve, which shows the usefulness of this technique in overcoming the limitations of previous antibiotic treatment. Right-sided endocarditis occurred classically in young patients (mean age, 36 yr), intravenous drug users in 50% of cases, and suffering more often from embolic complications. Finally, 5 cases without etiology or explaining factors were all immunocompetent male patients with previous aortic valvular lesions, and 3 of the 5 presented with an aortic abscess. Further investigations should be focused on this group to identify new agents of infective endocarditis.

Adolescent↗

PubMed2005

Bacteroides massiliensis sp. nov., isolated from blood culture of a newborn.

Gram-negative anaerobic rods were isolated from blood culture of a healthy baby born at term. Based on phylogenetic analysis and specific phenotypic characteristics, this strain was included within the Bacteroides cluster. The novel bile-resistant anaerobic species was designated Bacteroides massiliensis and it has 92.8 % 16S rRNA similarity to Bacteroides vulgatus and a DNA G + C content of 49 mol%. The major cellular fatty acid is anteiso-branched C(15 : 0). The type strain of B. massiliensis sp. nov. is B84634(T) (=CIP 107942(T) = CCUG 48901(T)).

Anaerobiosis↗

PubMed2005

Diversity of Borrelia burgdorferi sensu lato in Russian Far East.

Thirty strains of Borrelia burgdorferi sensu lato have been isolated from Ixodes persulcatus ticks and from skin lesions of Lyme disease patients in the Russian Far East from 1997 to 2003. We amplified full-length outer surface protein A (ospA) gene of all strains. BLAST search and following phylogenetic analysis showed that strains form four well-defined groups. Four strains belong to Borrelia afzelii species. Other strains distributed into tree major groups, identified as Borrelia garinii. Indeed, based on the ospA gene comparison, phylogenetic relationship of these groups among each other does not differ from relationship among other previously defined groups inside B. burgdorferi sensu lato genogroup, such as B. afzelii or Borrelia bissettii. Further investigations of genetic and serologic properties of the strains belonging to those groups are required in order to clarify their taxonomic status.

Animals↗

PubMed2005

Intracellular trafficking of Parachlamydia acanthamoebae.

Parachlamydia acanthamoebae is an obligate intracellular bacterium that naturally infects free-living amoebae. It is a potential agent of pneumonia that resists destruction by human macrophages. However, the strategy used by this Chlamydia-like organism in order to resist to macrophage destruction is unknown. We analysed the intracellular trafficking of P. acanthamoebae within monocyte-derived macrophages. Infected cells were immunolabelled for the bacteria and for various intracellular compartments by using specific antibodies. We analysed the bacteria colocalization with the different subcellular compartments by using epifluorescence and confocal microscopy. Bacterial replication took place 4-6 h post infection within acidic vacuoles. At that time, P. acanthamoebae colocalized with Lamp-1, a membrane marker of late endosomal and lysosomal compartments. A transient accumulation of EEA1 15 min post infection, and of rab7 and the mannose 6-phosphate receptor 30 min post infection confirmed that P. acanthamoebae traffic through the endocytic pathway. The acquisition of Lamp-1 was not different after infection with living and heat-inactivated bacteria. However, 24.5% and 79.5% of living and heat-inactivated P. acanthamoebae, respectively, colocalized with the vacuolar proton ATPase. Moreover, P. acanthamoebae did not colocalized with cathepsin D, a lysosomal hydrolase, suggesting that P. acanthamoebae interferes with maturation of its vacuole. Thus, P. acanthamoebae survives to destruction by human macrophages probably by controlling the vacuole biogenesis.

Acanthamoeba↗

PubMed2005

Characterization of the naturally occurring oxacillinase of Acinetobacter baumannii.

A chromosomally encoded oxacillinase, OXA-69, was characterized from Acinetobacter baumannii AYE. beta-Lactamase OXA-69 shared 97% amino acid identity with the recently described OXA-51 enzyme of A. baumannii and 62 and 56% amino acid identity with the carbapenem-hydrolyzing oxacillinases OXA-24 and OXA-23, respectively. Biochemical characterization of the purified OXA-69 revealed a narrow-spectrum hydrolysis profile but including, at a low level, imipenem and meropenem. By PCR and sequencing bla(OXA-69)-like genes were identified in all A. baumannii strains tested (n = 12), suggesting that this oxacillinase is naturally occurring in that species.

Acinetobacter baumannii↗

PubMed2005

Successive emergence of Enterobacter aerogenes strains resistant to imipenem and colistin in a patient.

Enterobacter aerogenes is an agent of hospital-acquired infection that exhibits a remarkable resistance to beta-lactam antibiotics during therapy. Five successive isolates of E. aerogenes infecting a patient and exhibiting a multiresistance phenotype to beta-lactam antibiotics and fluoroquinolones were investigated. Among these clinical strains, four presented resistant phenotypes during successive imipenem and colistin treatments. The involved resistance mechanisms exhibited by the successive isolates were associated with alterations of the outer membrane that caused a porin decrease and lipopolysaccharide modifications.

Anti-Bacterial Agents↗

PubMed2005

Correlation between ratio of serum doxycycline concentration to MIC and rapid decline of antibody levels during treatment of Q fever endocarditis.

Endocarditis is the major clinical manifestation of chronic Q fever. Although doxycycline along with hydroxychloroquine remains the mainstay of medical therapy for Q fever endocarditis, there are wide variations in the rapidity of the patient's decline of antibody levels during such therapy. We undertook a retrospective examination of whether there was any correlation between the ratio of serum concentration to MIC of doxycycline and response to treatment in patients with Q fever endocarditis. Included herein are 16 patients from whom Coxiella burnetii was isolated from cardiac valve materials. Serology and measurement of doxycycline and hydroxychloroquine serum levels were performed and recorded after 1 year of treatment. The MIC of doxycycline for C. burnetii isolates was determined using the shell vial assay in a real-time quantitative PCR assay. At the completion of a year-long therapy with doxycycline-hydroxychloroquine, all those that showed a low decline of antibody levels (n = 6) (i.e., <2-fold decrease in antibody titer to phase I C. burnetii antigen) had a ratio of serum doxycycline concentration to MIC between 0.5 and 1. In contrast, those having a ratio of > or =1 showed a rapid decline of phase I antibody levels (n = 9; P < 0.05). The only patient who died had a serum doxycycline-to-MIC ratio of <0.5, and the isolate of C. burnetii cultured from this patient was resistant to doxycycline (MIC = 8 microg/ml). The ratio of serum doxycycline concentration to MIC should be monitored during the course of therapy in patients with Q fever endocarditis.

Adult↗

PubMed2005

Intervening sequence acquired by lateral gene transfer in Tropheryma whipplei results in 23S rRNA fragmentation.

Completion of Tropheryma whipplei genome sequencing may provide insights into the evolution of the molecular mechanisms underlying the pathogenicity of this microorganism. The first postgenomic application was the successful design of a comprehensive culture medium that allows axenic growth of this bacterium, which is particularly recalcitrant to cultivation. This achievement in turn permitted analysis of T. whipplei RNA without contaminating eukaryotic nucleic acids. To obtain high-quality RNA, several extraction methods were compared, but under all conditions tested an atypical profile was observed. By using a Northern blot assay we demonstrated that an insertion sequence previously described in T. whipplei 23S rRNA is in fact an intervening sequence excised during maturation. This cleavage could involve an RNase III identified in the genome of this microorganism. Among the bacteria with a 23S rRNA insertion sequence, T. whipplei is the only gram-positive microorganism. We present phylogenetic evidence that this mobile genetic element was acquired by lateral gene transfer from another enteric bacterium.

Actinomycetales↗